A pop-up monitoring base station for seafloor heat flow includes a recovery unit, a discarding unit and a cable chopping mechanism. The recovery unit includes a recovery support, internally accommodating two acoustic release devices provided with closable hooks on bottoms thereof and loaded with floating balls. The discarding unit includes a discarding support, below which a heat flow probe is fixedly connected. The recovery unit and the discarding unit are fixed together through a steel wire rope with two ends connected with the closable hooks at the bottoms of the acoustic release devices. A cable extends from the discarding unit through the cable chopping mechanism fixed on the bottom of the recovery support and connects with the floating balls. The cable can be chopped off and/or pulled out automatically to realize successful separation between the recovery unit and the discarding unit.